Error in qr.fitted(qrhs, G) : 'qr' and 'y' must have the same number of rows

[cafferychen777]

hello,
when I run

species <- as.matrix(species)
print(dim(xy))
print(dim(as.data.frame(as.matrix(base@sam_data))))
print(dim(species))
print(adonis2(xy ~ species, data = as.data.frame(as.matrix(base@sam_data))))

I get Error in qr.fitted(qrhs, G) :
'qr' and 'y' must have the same number of rows

do you know why

[jarioksa]

No, I don't know. But you do not give many hints either. What are xy, species and base@sam_dataand what are their dimensions? Moreover, the RHS of formula (~ species) should be names of variables found in data.

[cafferychen777]

xy is a matrix just like this
Comp 1 Comp 2
Sample1 3.626698584 1.86298075
Sample2 -1.006893073 -3.19403722
Sample3 0.082060143 2.47763831
Sample4 -0.748028447 -2.98723273
Sample5 -1.328411860 1.72429651
Sample6 1.798678420 0.52244040
Sample7 1.074809402 0.88641367
Sample8 -0.529578562 -0.95244148
Sample9 -4.789023081 0.21641650
Sample10 -1.043885947 2.48610885
Sample11 -0.007122425 0.82511560

xy has the same rows as data.
data is the label data.frame.
species is one col in data.

I try to change rhs to name of variable. But I use adonis2 in a function. I change character to a variable name to achieve it. But Error in model.frame.default(delete.response(terms(formula)), data, na.action = na.action) :
object is not a matrix

My code is

adonis2(xy ~ as.symbol(colnames(as.data.frame(as.matrix(simphyseq@sam_data)))), data = as.data.frame(as.matrix(simphyseq@sam_data)))

What are your insights?
Thank you so much!

[jarioksa]

I really do not understand how you came up with such a long and winding expressions. What do you think they make? It seems that as.symbol(colnames(as.data.frame(as.matrix(simphyseq@sam_data)))) expands to the name of the first variable in data. I suggest that instead of packing together such complicated expressions, you evaluate these to simple structures before calling adonis2. Then you can also see if these expressions really do what you think they should do. That is, see what you get from

xy # is this a matrix, what are its dims
as.symbol(colnames(as.data.frame(as.matrix(simphyseq@sam_data)))) # what is the name you get here
as.data.frame(as.matrix(simphyseq@sam_data)) # does this exist, what are its dims

Also remember that as.symbol returns only the first element of a vector, or one single name. You can see this by comparing output of letters and as.symbol(letters).